The Two Year Secret
by Sherlockian87
Summary: A different twist on what happened when Sherlock returned from the dead.


**This is for Sweet-Sweet-Escape aka MaybeItsJustMyType**

 **Her poor little boy was sick with a high-fever, and for some reason that gave my brain this idea!**

 **Hope you like it Sweet's :)**

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Molly Hooper was tired. She had had a long day, four autopsies and a mountain of paperwork that she had barely made a dent in. But her shift was now over and she was able to go home. She strode into the locker room, and opened hers. When the mirror caught the reflection of someone standing behind her she quickly spun about, the jolt of fear immediately turning into a jolt of happiness.

"Sherlock!" she breathed out.

Before he was even able to open his mouth to speak she had thrown herself at him. He caught her and cradled her close, burying his nose in her hair, breathing in the familiar scent of her; the scent that was purely Molly Hooper.

"Sherlock, Sherlock, Sherlock!" she murmured, her face buried in his chest as she clung to his Belstaff. "Are you back for good?"

When she felt him nod in affirmative, the feeling of relief flooded through her veins. She stepped back, but they still held onto each other. He reached up and slowly brushed his fingertips across her cheek.

"May I?" he asked her, his eyes flitting down to her lips before meeting her gaze once more.

She nodded. He kissed her, gently at first, slowly, but it soon grew in passion. By the time that they parted he had her pressed up against a nearby locker. He leaned his forehead against hers, looking into her eyes.

"I've missed you so much Sherlock," she said to him.

He brushed the tip of his nose against hers. "I've missed you too."

His hands had slipped beneath her lab coat, caressing her sides. Suddenly he looked confused. "Molly you - you feel different. You -" he stepped back and looked her over, she kept silent beneath his observant gaze. "You've had a baby."

A flush traveled from her neck to her cheeks. "Yes. I have."

His eyes snapped up to meet hers. He slowly slipped his hands out from the lab coat and took a single step back. "You're with someone then?"

She shook her head and moved closer to him, stretching her hand out to him. "It's not like that, it's not like that at all. Having an almost-two-year-old puts a bit of a damper on the attraction." Molly stood silent as she watched Sherlock's mind whirl and twirl over what she had just said.

"Nearly two ...?" he choked out.

She took another step closer, placing her hand on his arm. "Yes. She's yours."

He blinked rapidly, his eyes slightly unfocused. "She?"

"Yes. We have a daughter."

He swallowed. "You mean that night ... before I left ...?"

Molly nodded.

His brow furrowed, a crinkle forming above his nose. "But I wore a condom!" he spat out.

"I know Sherlock ... but they don't prevent 100%."

He sniffed. "Clearly not." His expression quickly softened and he reached out to pull her close. "We have a daughter!" he said to her, his eyes sparkling.  
Molly nodded, smiling. Suddenly his expression tightened and he gently released her.

"How dare Mycroft not tell me! How dare he keep such a thing from me!" Sherlock was stalking up and down the room now, his hands clenching and unclenching.

"Please don't be angry with Mycroft! If you want to be angry with someone, then be angry with me."

Sherlock spun about, facing her. "You? Why should I be angry with you!?"

"Because I asked Mycroft not to tell you. I begged him not to. I didn't want you to be distracted," she explained.

With three long strides, Sherlock was once more in front of her. He kissed her deeply, pressing her up against him. "Molly, you are the most unselfish person I have ever met!" he said to her before he kissed her again, cradling her close. "Does she ... does she have my last name?"

Molly nodded, her arms slipping around his waist beneath his coat. "Mycroft insisted."

Sherlock frowned. "You didn't want to give her my name?"

Molly dropped her gaze from him. "I didn't want to assume anything."

He sighed, resting his cheek upon the top of her head.

She new the silent question that he was thinking. "I named her Elizabeth Violet Holmes."

"Hmm ... Elizabeth after your mother, and Violet after mine."

"Yes."

"I like it."

"Good. I'm glad, I was worried you wouldn't."

He pressed a kiss to her hair. "Does ... everyone know?"

Molly's arm's tightened about his waist. "I haven't seen John ... since the funeral. But Mrs. Hudson knows, and of course Lestrade. John has been, very distant. I don't know how happy he'll be to see you."

Sherlock humphed, and she gave his side a slight pinch.

"It's been very difficult for him. He's had to grieve for you; he's been thinking all this time that you're gone. Don't expect the same warm welcome that you got from me."

Sherlock let out a snort. "I should hope not, I don't want to kiss him!"

In spite of herself, Molly giggled, tilting her head back. Sherlock was smiling down at her. He cupped the side of her face in his hand.

"You haven't had an easy time of it either. Caring for a child all alone," he said softly.

She closed her eyes and leaned into his palm. "I've not been entirely alone. Your brother has been wonderful, and so have your parents. I don't know what I would have done without them."

"Well, you're not alone now."

Molly's eyes opened just as he pressed his lips to her forehead.

"May I see her? She's here, isn't she?" he asked.

"Yes, she's in the crèche."

He frowned, thinking for a moment. "Perhaps I shouldn't see her for the first time here ... I think I'd prefer not to."

Molly nodded in agreement.

"I'll come to your flat tonight, after I've seen Mrs. Hudson and John."

"Ok."

He cradled her head in his hands and kissed her deeply. "Until tonight."

She placed her hands over his. "Tonight."

They kissed once more before he strode from the locker room.

* * *

Later that evening Molly was just settling down with a well-deserved cup of tea when there was a sudden, desperate knocking at her door.

"Molly!"

It was Sherlock. And his voice sounded strange, almost as if he had a cold. She jumped to her feet and quickly opened the door. When she took in the sight of him, she let out a soft gasp, her hand covering her mouth. He was holding a cloth to his face, his head tilted back slightly. He was covered in blood, and it was still faintly dripping from his nose.

"What happened?" she asked as he stepped inside.

"John," was his muffled reply.

She helped him take off his Belstaff before going to get her first-aid kit as he collapsed onto her sofa. Upon getting the kit she sat down beside him.

"I did warn you," she said.

Sherlock let out a hmph then groaned. She took away the bloody cloth and placed it on the lid of the box as he leaned back into the cushions.

"Let me clean you up." She wiped away the blood, putting a bit of antiseptic on his split lip, thankful that his nose had stopped bleeding. "I don't think you'll bruise," she said before placing a gentle kiss on his cheek.

He pouted. "That's not where it hurts."

She chuckled. "Where does it hurt then?"

He pointed to his lips. Molly shook her head but gave him a quick kiss. When she pulled away he was still pouting.

"Why didn't you answer my texts?" he asked her.

"You texted me? Sorry, I didn't know. I've been trying to get Lizzie to settle down ever since we got home."

Sherlock took in Molly's tired, frazzled state. "She's unwell?"

Molly nodded. "Just a low fever, but she's fussy. I only just got her to sleep." Her gaze drifted down to his chest. "There's blood on your shirt, I think I may have a t-shirt or two of yours here. Let me go check." She stood and walked down the hall.

Sherlock leaned forward and began to undo the buttons of his shirt, just as she returned he was pulling it off. She stood, staring at him, taking in the sight of the bruises and cuts that covered his torso. He winced slightly.

"Don't fret Molly; they look worse than they feel."

She was still frowning as she sat back down beside him, holding out his t-shirt. He took it and slipped it on before he leaned back against the cushions, sighing deeply. He patted the spot next to him. Molly moved closer and he slipped his arm around her waist.

"Who am I to think that I've had a rough time these passed two years?" she said quietly.

He nudged her closer and she laid her head upon his chest. Before either one of them could say anything the sounds of Lizzie's cries filled the room, coming from the baby monitor that was sat upon the coffee table.

"Damn," Molly muttered. She struggled to her feet and moved down the hall, Sherlock close behind her.

"You have her in the spare room?" he asked, as Molly opened the door, the sound of their daughter's cries growing louder.

"Mmhm, this room is a bit warmer, mine is always freezing," she explained as she approached the cot. "It's all right sweetie, mummy is here." She picked up the crying child, holding her close and swaying side to side as she whispered soothing words to her. "You can come in Sherlock; you don't have to stand in the doorway. Come and meet your daughter." Lizzie was still crying, but not as loudly.

Sherlock stepped into the room and slowly approached them. Molly turned so that their daughter could see him. Lizzie instantly stopped crying, staring at him.

Molly smiled. "Ohhhh I think she knows you're her daddy!" She pressed a kiss to her rosy cheek. "That's my smart girl!"

Sherlock stared at her as if he was bewitched.

"I pretty sure she's going to have your curls," Molly noted.

"She has your nose."

Lizzie stretched her hands out to him, Molly's smile widening.

"She wants you to hold her!"

Sherlock moved closer to them, and Molly handed her over. Lizzie comfortably settled into his arms, staring up at him with wide, curious eyes.

"Hello Elizabeth, I'm Sherlock. Your father."

Molly wiped at her eyes as they filled with tears. Lizzie cooed with delight, waving her tiny fists. Sherlock was smiling, his eyes glistening.

"If you rock her gently back and forth, she should fall asleep," Molly said to him.

He began to move from side to side, slowly. He couldn't stop staring at the little girl in his arms. "She's amazing Molly, absolutely amazing."

Molly moved closer to them, laying her head on his arm as she swayed in time with him. "She is, isn't she?"

Lizzie snuggled herself against him, almost instantly falling asleep. Molly gently stroked her cheek with her fingertip then felt her forehead.

"Her fever is breaking."

Sherlock placed a gentle kiss to the downy head. After a few more minutes he moved over to the cot and gently laid her down. He wanted to keep her in his arms, but there were things he needed to discuss with Molly, important things. She gently brushed back Lizzie's hair and covered her with a blanket before they quietly left the room.

Once the door was closed behind them, Molly pulled him into her arms. He held onto her tightly.

"Thank you Molly," he murmured softly.

She tilted her head back and stood on her tiptoes so that she could give him a gentle kiss. "You're welcome."

They stared silently at each other for several moments.

"Are you staying the night?" she asked him.

"If you want me to."

She smiled. "I want you to."

They moved into her bedroom, and she switched on the baby monitor. Sherlock toed off his shoes, removing his socks before undoing the button and zip of his trousers. Molly changed into her pyjamas and Sherlock stopped, one leg still in his trousers, drinking in the sight of her. Her body had changed since giving birth to Lizzie; she was softer, rounder, but still very much so _Molly_. She walked over to the bed and sat down upon the mattress. Realizing that he was still standing with his leg in the air, he quickly finished undressing, leaving himself in just his pants and his t-shirt. He moved towards the bed and she looked up at him.

"It will be nice not to sleep alone for once," she said.

He smoothed his hands over her arms. "You haven't been with anyone?"

She shook her head. "No. Well, there was this one guy Tom. We only went on two dates, and when he found out I had a daughter ... that was the end of it."

"Coward."

Molly giggled. "He was a bit of an idiot." She scooted herself back and Sherlock got onto the bed. She lay down and he stretched out beside her. "There were a few others that asked me out, but none of them were you, they didn't matter. They weren't who I wanted."

Sherlock kissed her, quickly covering his body with her own. "Molly," he murmured between kisses, "I want us to be a proper family. Move in with me, please? I want to take care of you. I need to make up for all the time that I've missed."

She kissed him hungrily. "We'll talk more properly about this in the morning," she told him breathlessly.

He nodded and kissed her again. When her hands began to wander, drifting downwards, he grabbed them and pulled them away.

"Molly!" Her name came out in a rush as he struggled for breath. "I want you, I truly do, I've missed you so much, but I think it's best if we wait. You're exhausted, I know you are."

She nodded in agreement and he gave her lips a gentle kiss before moving off of her. She tucked herself close up against him, sighing happily. "You have a lot of lost time to make up for mister," she said in a teasing tone as she gently poked him.

He chuckled, moving onto his side so that he was facing her. "I have every intention of doing so," he told her. "That one night was most definitely not enough to sate my desire for you." He kissed her. "Besides, haven't you always said you wanted at least three children?" He moved his mouth to her neck, smiling against her skin as she laughed.

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 **As always, please leave a review! I do love them so :D**

 **Tumblr? I'm on there as sherlockian87**


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